After weeks of deliberation, the Supreme Court Friday rebuffed the White House and extended an Obamacare exemption for a group of nuns who claim that provisions of the Affordable Care Act infringe on their religious liberties. As a result of the court’s order, the nuns will not have to choose between either large fines or compliance with Obamacare’s procedures for religious organizations that object to providing contraceptive coverage to their employees, at least until a lower court rules on the merits of the case.

Two clues suggest the nine Supreme Court justices fought a behind the scenes battle over the order.

First, the courts decision took a long time. The initial exemption was issued in response to an emergency request from the Little Sisters of the Poor by Associate Justice Sonia Sotomayor hours before Obamacare requirements were due to go into effect last New Years Eve. Sotomayor said the exemption would stand until the administration responded to the nuns’ objections and the court further weighed the matter. That last step ended up taking three weeks, an unusually long time for a procedural matter at the court.

Second, when the court finally did decide how to proceed late this week, the order it issued seemed conflicted. On the one hand, the nuns got what they wanted: the order means they don’t have to certify that their religious beliefs prevent them from complying with Obamacare’s requirement that employers cover contraceptive costs. The nuns said by certifying their objections, they might be enabling others, including third party insurers, to provide contraceptive coverage.

On the other hand, the court said that to get the extended exemption the nuns have to write to Secretary of Health and Human Services Kathleen Sebelius informing her that they are a non-profit organization that has “religious objections to providing coverage for contraceptive services.” That certification hardly differs from what Obamacare would require of the nuns in the first place.

A lawyer for the nuns said they were “relieved and delighted” at the court’s action. “It means that the Little Sisters can have their day in court without paying millions in fines,” says Daniel Blomberg, legal counsel at the Becket Fund, a non-profit legal organization representing the nuns. He said the order’s requirement that the nuns inform Sebelius of their objections has “no strings attached” so does not infringe on their religious liberties the way certifying their objections under Obamacare would. The Justice Department did not immediately comment on the order.

The court’s lengthy deliberation over the order and its ultimate insistence that the nuns certify their continuing objections in writing suggests the case has legs. Once the lower court rules on the merits of the nuns’ objections, the loser will presumably ask the Supreme Court to rule on the dispute. Even if the court takes the case and rules against the White House, however, a relatively small number of Americans would be exempted from Obamacare, and the ruling would not likely affect the broader implementation of health reform.